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OfflineEarthspirit
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Organic Chemistry * 5
    #20417408 - 08/14/14 10:53 AM (9 years, 5 months ago)

Introduction to Organic Chemistry

Carbon is the sixth element on the periodic table and is truly remarkable. The atomic structure of carbon allows it to form stable, covalent bonds1 with other carbon atoms. This allows the formation of a nearly limitless number of carbon compounds. If you can think up a structure of carbon-to-carbon bonds, somewhere in our vast universe that compound probably exists. Some of the various allotropic2 forms that carbon can take are graphite, diamond, and buckminsterfullerene. If you could see the individual atoms of graphite, it would appear that they were arranged as flat sheets layered upon each other. These sheets have the ability to slide over each other, leading to the smooth feeling of graphite as it glides over various substances, like paper, for example. Diamond has a three-dimensional structure (as opposed to the 2D graphite sheets) giving it its characteristic hardness. Indeed, it is one of the hardest natural substances known to man. Molecules of buckminsterfullerene would look like soccer balls, if you could magnify them enough to see.


(http://chem-test-review.weebly.com/uploads/2/4/4/3/24430149/1604703_orig.jpg)


Carbon can also form stable bonds with other elements leading to the formation of compounds such as alcohols, ketones, aldehydes, esters, etc. These compounds can all have vastly different properties depending on their structure. For example, ethanol is a widely used intoxicant of little harm if used in moderation by a healthy person. It is composed of two carbons, six hydrogens, and one oxygen, or C2H6O. Methanol, by contrast, is dangerous in any amount, potentially causing blindness or death. The difference between the two compounds? One less carbon and two less hydrogens, or CH4O.


a)methanol b)ethanol
(http://cnx.org/content/m39455/1.1/CG12C1_055.png)


The last property of carbon that I’ll mention is it’s ability to form double or triple bonds with other carbon atoms. These are known as alkenes and alkynes, respectively. All these properties make carbon one of the most interesting elements in the universe. The study of carbon is so vast and important to our species (we are carbon-based lifeforms, after all) that we’ve dedicated an entire branch of chemistry to it. Organic chemistry is essentially the study of carbon and the compounds composed of it. Every bit of food (not including water) and almost every medication/drug that a person puts into his/her body is a compound of carbon. Nearly everything in our man made environments are also (plastics, rubbers, fibers, etc.). It’s easy to see why studying this subject is so practical for many various fields and careers.



(http://www.aspirin-foundation.com/graphics/photos/aspirin.gif)


I’m very excited to teach this course and I’ll have more lessons coming soon that are less encyclopedic. My goal is to start basic (absolute beginners) and get more advanced as we go through the lessons. I’ll also be throwing in some short lessons on general chemistry to discuss topics like determining molar mass or the discussion of inter- and intra-molecular bonding or anything else I happen to feel is relevant.


1. Covalent bond - the sharing of a pair of electrons between atoms
2. Allotropy – the tendency of certain elements to exist in more than one form



References:

All information is referenced from the book General, Organic, and Biochemistry, 7e by Katherine J. Denniston, Joseph J. Topping, and Robert L. Caret


Edited by Earthspirit (08/14/14 11:16 AM)


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OfflineSmokey-hitz
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Re: Organic Chemistry [Re: Earthspirit] * 3
    #20417412 - 08/14/14 10:54 AM (9 years, 5 months ago)

ill be watching this thread


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Offlineflower_child
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Re: Organic Chemistry [Re: Smokey-hitz]
    #20426890 - 08/16/14 11:37 AM (9 years, 5 months ago)

Looking forward to this thread!


--------------------
Today while walking up the stairs
I met a man who wasn't there
He wasn't there again today
Oh how I wish he'd stay away


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Offlinemaasenmuhaasen
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Re: Organic Chemistry [Re: flower_child]
    #20438915 - 08/18/14 06:50 PM (9 years, 5 months ago)

I'm in this class!  I love OChem, but it's pretty difficult.  I recommend simple guides to reaction mechanisms, substitutions/eliminations, syntheses, etc as these are a lot of things to memorize!


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OfflineDorfnob
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Re: Organic Chemistry [Re: maasenmuhaasen]
    #20439001 - 08/18/14 07:03 PM (9 years, 5 months ago)

:popcorn:


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Offlinemagickspore
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Re: Organic Chemistry [Re: Dorfnob]
    #20442895 - 08/19/14 02:22 PM (9 years, 5 months ago)

Quote:

Dorfnob said:
:popcorn:




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Offlinealexpg
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Re: Organic Chemistry [Re: magickspore]
    #20453972 - 08/21/14 01:12 PM (9 years, 5 months ago)

Sounds great looking forward to the lessons. :thumbup::thumbup: :like:


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Offlinekmetric
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Re: Organic Chemistry [Re: alexpg]
    #20482094 - 08/26/14 11:32 PM (9 years, 5 months ago)



Awesome..I'm in as well.


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Offlinejsncrs
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Re: Organic Chemistry [Re: kmetric]
    #20482211 - 08/27/14 12:04 AM (9 years, 5 months ago)

I'm in. Always wanted to learn this shit.


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Invisible4HO-DMT
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Re: Organic Chemistry [Re: Earthspirit]
    #20482261 - 08/27/14 12:19 AM (9 years, 5 months ago)

You got me, hook, line and sinker. I'm eager to learn more. :tripmolecule:


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Offlinejsncrs
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Re: Organic Chemistry [Re: jsncrs]
    #20482377 - 08/27/14 12:57 AM (9 years, 5 months ago)

Wondering if anyone can answer this quick question, why is Ethanol written as C2H6O, but in the Aspirin image, the structure is written as OCOCH3? does that mean that aspirin could be shown as C2O2H3? is it just a different way of writing it? hope that makes sense. Awesome thread btw, can't wait for more.


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OfflineIce9
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Re: Organic Chemistry [Re: jsncrs]
    #20483343 - 08/27/14 09:39 AM (9 years, 5 months ago)

jsncrs, the first one C2H6O is the molecular formula, and only conveys information on the number of different atoms in a molecule (an it's formula weight by extension).  The second is a form of shorthand when drawing a chemical structure used in place of drawing out common chemical structures, in this case the acetyl group.  The OCOCH3 indicates not only what kind and how many atoms, but also their connectivity to each other, in this case
-O-C(=O)-CH3.  Hope this helps.


--------------------
The reasonable man adapts himself to the world; the unreasonable one persists in trying to adapt the world to himself. Therefore, all progress depends on the unreasonable man. -- George Brenard Shaw


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Offlinejsncrs
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Re: Organic Chemistry [Re: Ice9]
    #20485561 - 08/27/14 06:59 PM (9 years, 5 months ago)

Quote:

Ice9 said:
jsncrs, the first one C2H6O is the molecular formula, and only conveys information on the number of different atoms in a molecule (an it's formula weight by extension).  The second is a form of shorthand when drawing a chemical structure used in place of drawing out common chemical structures, in this case the acetyl group.  The OCOCH3 indicates not only what kind and how many atoms, but also their connectivity to each other, in this case
-O-C(=O)-CH3.  Hope this helps.




Ah, makes sense! thanks for clearing that up :smile:


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Invisible4HO-DMT
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Re: Organic Chemistry [Re: Earthspirit]
    #20486779 - 08/27/14 11:46 PM (9 years, 5 months ago)

Earthspirit, will you show us a simple synthesis?


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Invisibleazur
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Re: Organic Chemistry [Re: 4HO-DMT]
    #20486792 - 08/27/14 11:49 PM (9 years, 5 months ago)

Present


--------------------


A cube is NOT a cube.

FALL IN LOVE WITH LC
FOTTSE!!!
ALL NOOBS READ THIS!!!



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OfflineGorlax
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Re: Organic Chemistry [Re: 4HO-DMT]
    #20486821 - 08/27/14 11:57 PM (9 years, 5 months ago)

That's a hard question. There's a million different synthesis techniques.

You got your major ones like Substitution reactions and elimination reactions. Then you got aldol condensations and hydrolysis. Then you got random ones teachers just want to teach you.

This is really hard topic that kind of needs buildup before you can get a hang of the material. I'd probably start with periodic table and valence electrons and that non-sense.


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InvisibleBiodiversity
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Re: Organic Chemistry [Re: Gorlax]
    #20499066 - 08/30/14 07:06 PM (9 years, 4 months ago)

Posting to receive updates.


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OfflineTrentcoat
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Re: Organic Chemistry [Re: Biodiversity]
    #20507837 - 09/01/14 08:12 PM (9 years, 4 months ago)

can't wait for the recrystallisation section. purity is king. and if I could ask if you could explain the pH calculation for a acid base extraction. I am a little bit fuzzy on what determines the pH in the initial extraction into h20,then into hydrochloric acid then to naphtha. I'm sure you will explain, and please anyone with suggestions on solvents, acids and bases Thanks


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Invisibleazur
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Re: Organic Chemistry [Re: Trentcoat] * 1
    #20507861 - 09/01/14 08:18 PM (9 years, 4 months ago)

Teacher.....


--------------------


A cube is NOT a cube.

FALL IN LOVE WITH LC
FOTTSE!!!
ALL NOOBS READ THIS!!!



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Offlinepsychedelicbath
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Re: Organic Chemistry [Re: azur]
    #20511602 - 09/02/14 07:20 PM (9 years, 4 months ago)

more!


--------------------
The human being is part of a whole, called by us the "universe", a part limited in time and space. He experiences himself, his thoughts and feelings, as something separate from the rest - a kind of optical delusion of his consciousness. This delusion is a kind of prison for us, restricting us to our personal desires and to affection for a few persons nearest us. Our task must be to free ourselves from this prison by widening our circles of compassion to embrace all living creatures and the whole of nature in its beauty.
    - Albert Einstein


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OfflineEarthspirit
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Re: Organic Chemistry [Re: psychedelicbath] * 2
    #20516986 - 09/03/14 10:55 PM (9 years, 4 months ago)

Hello all!

Wow! I'm excited to see all these prospective students. I thought this thread was going to be a wasteland. I have to apologize for not posting in a more timely manner - I have been very busy with work and school. I've decided to alter my original goal for this thread. I'm going to start off the lessons with some introductory general chemistry concepts. I was going to jump straight into organic chemistry, but, as I was organizing the lessons, I realized that there are probably a lot of topics that are going to be very confusing to readers without some general chemistry background. Again, though, my goal is to provide a basic education of general and organic chemistry. I do not, at this point, plan to include elaborate chemical procedures or analyses in the lessons, but I will, if so requested. My lessons are directed toward beginners, but will advance in complexity as the lessons unfold. I also plan to include hands-on experiments in some of these topics.

Tomorrow, I'll follow up on this post with a basic course outline and the first lesson "Introduction to Matter and Energy".

I did get a few questions though, which I am happy to answer.

Quote:

4HO-DMT said:

Earthspirit, will you show us a simple synthesis?




Gorlax is correct. There are many, many different synthesis techniques and processes. I do want to point out, though, that substitution reactions1 and elimination reactions2 are separate and distinct procedures (not categorized as synthesis reactions3) . I will explain those in more detail in the future, but, for now, the basic formula for a synthesis reaction is A + B --> AB. In other words, two simple substances combine to make a third substance composed of the two reactants4.

A classic example is the synthesis of sodium chloride from atomic5 sodium and chlorine gas. In the reaction, sodium cations6 combine with chlorine anions7 to reach a compound of neutral charge. (Positively charged atoms attract negatively charged atoms -- think magnets)

2 Na + Cl2 --> 2 NaCl 


or

Na+ + Cl- --> Na+Cl-
(Chlorine does not exist freely in the atomic state. It exists in the molecular8 state in nature, so one of these atoms is taken from the molecular form of the element, hence the top equation.)


Everyone is familiar with sodium chloride -- it's table salt. What's remarkable about this reaction is that sodium and chlorine gas are both extremely reactive and poisonous. It would not take much at all to kill a person. The product of the reaction, however, is relatively
harmless. This is a great example of how only 98 naturally occurring elements can result in the enormous diversity of matter present in our universe.

Terms:
1. Substitution reaction (or single displacement reaction) -- One element replaces another in a compound. A + BC --> AC + B
2. Elimination reaction -- reaction that results in the removal of an atom or ion from a compound.
3. Synthesis reaction -- a reaction in which two simple substances are combined to make a more complex substance.
4. Reactants -- the initial substances in a chemical reaction, written on the left side of the chemical equation.
5. Atomic elements-- exist in nature with single atom elements as their basic units.
6. Cation -- an atom that has lost an electron, resulting in a positive charge.
7. Anion -- an atom that has gained an electron, resulting in a negative charge.
8. Molecular elements -- exist in nature with the basic unit of two atoms bonded together.


All information sourced from Introductory Chemistry: 4e by Nivaldo J. Tro and General, Organic, and Biochemistry: 7e by Katherine J. Denniston, Joseph J. Topping, and Robert L. Caret.
Photo credit: http://faculty.clintoncc.suny.edu


P.S. I got to this post late tonight. I'll answer the other question on pH calculation tomorrow when I continue the lessons.


Edited by Earthspirit (09/04/14 05:11 AM)


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Invisible4HO-DMT
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Re: Organic Chemistry [Re: Earthspirit]
    #20517543 - 09/04/14 01:43 AM (9 years, 4 months ago)

Thank you, Earthspirit.


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Offlines240779
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Re: Organic Chemistry [Re: Earthspirit]
    #20521273 - 09/04/14 09:09 PM (9 years, 4 months ago)

subbed


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OfflineKingKnowledge
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Re: Organic Chemistry [Re: s240779]
    #20522970 - 09/05/14 06:03 AM (9 years, 4 months ago)

Quote:

Da2ra said:
subbed




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Offlinekmetric
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Re: Organic Chemistry [Re: KingKnowledge]
    #20525953 - 09/05/14 09:24 PM (9 years, 4 months ago)



Thanks Earthspirit. Will be following this thread eagerly. Can't wait for the hands-on stuff you have planned as well.


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Offlines240779
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Re: Organic Chemistry [Re: s240779]
    #20533983 - 09/07/14 03:14 PM (9 years, 4 months ago)

I'd like to understand why the -codone and -morphone opioids are harder to synthesize than heroin ->

Processing thebaine to other narcotic alkaloids is not something that can be done in a home lab. I have yet to see e.g. clandestine oxycodone production or large scale thefts of catalytic hydrogenation equipment...

sekio - http://www.bluelight.org/vb/threads/579880-Questions-about-opiate-synthesis?p=9776254&viewfull=1#post9776254


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Offlinekmetric
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Re: Organic Chemistry [Re: s240779] * 1
    #20617317 - 09/25/14 01:55 PM (9 years, 4 months ago)

Hope you're still around Earthspirit was really looking forward to this..

:feelingblue:


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OfflineGdivski
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Re: Organic Chemistry [Re: kmetric]
    #20624700 - 09/27/14 08:10 AM (9 years, 4 months ago)

Carbon hold the key to all life form as we know it.
Carbon is the balance that gives us the beautiful plant we live on. The only one we know that holds intelligent life.
Great post


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InvisibleZombi3
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Re: Organic Chemistry [Re: Gdivski]
    #20624703 - 09/27/14 08:11 AM (9 years, 4 months ago)

Bookmarked:awesomenod:


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Invisibleazur
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Re: Organic Chemistry [Re: Zombi3]
    #20624830 - 09/27/14 08:59 AM (9 years, 4 months ago)

More please


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A cube is NOT a cube.

FALL IN LOVE WITH LC
FOTTSE!!!
ALL NOOBS READ THIS!!!



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Offlineblojo02184
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Re: Organic Chemistry [Re: azur]
    #20634238 - 09/29/14 08:24 AM (9 years, 3 months ago)

:popcorn:


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Offlinemusiclover420
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Re: Organic Chemistry [Re: blojo02184] * 2
    #20647296 - 10/02/14 02:25 AM (9 years, 3 months ago)

Bring us more organic chemistry knowledge, this thread is such a cool idea.


--------------------
Don't worry about me, I've got all that I need. And I'm singing my song to the sky

You know how it feels, With the breeze of the sun in your eyes. Not minding that time's passing by

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I talk to myself, I need nobody else. I'm lost and I'm mine, yes I'm free



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Offlineuglyman
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Re: Organic Chemistry [Re: musiclover420]
    #20765827 - 10/28/14 09:26 PM (9 years, 3 months ago)

Thank you for posting this. I've looked into organic chemistry before and it starts off easy but I always end up getting confused. I'll definitely be watching and reading this thread.


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InvisibleRazzldazzle

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Re: Organic Chemistry [Re: uglyman]
    #20778431 - 10/31/14 08:49 PM (9 years, 2 months ago)

So 2Na + Cl2 = 2NaCl. Its a synthesis reaction yes? How do you go from the reactants to the product? I don't understand how Cl2 goes to just 1 Cl in the product. Thanks!


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OfflineThebooedocksaint
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Re: Organic Chemistry [Re: Razzldazzle]
    #20778895 - 10/31/14 10:56 PM (9 years, 2 months ago)

...Not organic chemistry. That's ionic bonding, organic is almost exclusively a study of bonds more in the covalent spectrum.

I think one can use green light to generate Cl. Radicals which want to bond or grab an electron very bad.

I've taken Organic I and II and got an A, but I'd hardly consider myself an expert to teach any of it.


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InvisibleK1ngSp4de
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Re: Organic Chemistry [Re: Thebooedocksaint]
    #20870441 - 11/21/14 01:01 PM (9 years, 2 months ago)

:popcorn:


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                                    PC Repair and Troubleshooting Forum

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Offlineafrekcan
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Re: Organic Chemistry [Re: Earthspirit] * 1
    #20887183 - 11/25/14 02:38 AM (9 years, 2 months ago)

I hate to hijack, but I figured since the OP hasn't replied in quite a while I might help string this thread along...(if anyone shows interest I'll happily continue...)

AN INTRODUCTION TO BOND LINE STRUCTURES

A very common way of representing organic compounds is known as the bond line structure, which is essentially a shorthand method of drawing organic compounds that does not explicitly label carbon or hydrogen atoms. In order to advance in organic chemstry, it is important to understand what these representations mean in terms of molecule's structure and composition. Below is the bond line structure of butane, with carbon atoms circled.
(Apologize for shitty ms paints)




However, if we were to draw all the atoms, the structure would actually look like this:



Some important points to note:

-Each kink or end of a line (circled in red in first image above) represents a carbon atom. Each carbon atom can have up to four bonds (four lines connecting to other atoms, each indicating the sharing of an electron pair).

-In bond line strutures, hydrogen atoms are implicit, thus, if a carbon is
shown bonded to two other atoms, then there are two hydrogen atoms not shown.

-If a carbon is shown bonded to three other atoms, then one hydrogen is not shown, ect.

Nomenclature - IUPAC (International Union of Pure and Applied Chemistry)

Carbon chains that contain only single bonds, such as butane shown above are known as alkanes, and are named with the suffix -ane. The prefix is based off of the number of carbon atoms the structure contains:

meth- 1
eth- 2
prop- 3
but- 4
pent- 5
hex- 6
hept -7
oct -8
non -9
dec- 10
undec- 11
dodec- 12
cont...

-Practice:
Name the following:



Edited by afrekcan (11/25/14 01:36 PM)


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InvisibleRazzldazzle

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Re: Organic Chemistry [Re: afrekcan]
    #20888273 - 11/25/14 11:59 AM (9 years, 2 months ago)

Would that be hexane?


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Offlineafrekcan
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Re: Organic Chemistry [Re: Razzldazzle]
    #20888886 - 11/25/14 02:15 PM (9 years, 2 months ago)

Correct.


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InvisibleRazzldazzle

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Re: Organic Chemistry [Re: afrekcan]
    #20889225 - 11/25/14 03:25 PM (9 years, 2 months ago)

Cool, got any more lessons? Thanks for that BTW.


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Offlineafrekcan
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Re: Organic Chemistry [Re: Razzldazzle]
    #20890124 - 11/25/14 06:20 PM (9 years, 2 months ago)

NOMENCLATURE OF BRANCHED ALKANES

Carbon chains can also form more complicated structures with numerous branches. This section will (briefly) cover the systematic method for naming these types of compounds.

General Procedure:

Step 1 - Identify the longest consecutive chain (the one consisting of the most carbon atoms). This is referred to as the parent chain. Other branches that are attached to the parent chain are called substituents.



In cases where there appears to be more than 1 possible parent chain, we use the one with the greatest number of substituents. Below the correct parent chain is highlighted in red, and an incorrect choice is highlighted in blue.





Step 2 - Name the parent chain and the substituents.
This is done according to the general rules previously described for simple alkanes.



Step 3 - Assign the position of each substituent.
Now we need to number each carbon of the parent chain such that the substituents are placed at the lowest possible number.



Step 4 - Writing the name.

The basic formula for writing systematic names is as follows (X is a placeholder for substituent location):

X,X,X-(first substituent)-X,X,X-(second substituent)(parent name)

(there can be many more substituents but only 2 are shown above for simplicity)



Example walkthrough:

What is the systematic name of the compound below?



First identify the parent chain (highlighted in red below). In this case, it contains 9 carbons, so it is called nonane.
Now identify the four substituents (circled in green) by counting the number of carbon atoms. Substituents are named using the same prefix as a typical alkane but are given the suffix -yl. When determining the name of a substituent, be careful not to count any of the carbon atoms that are part of the parent chain.



Now we number each carbon of the chain. Note where we begin counting in this case, it would be incorrect if we had began at the opposite end.



Correct numbering:

Ethyl at carbon #6

2x Methyl at carbon #3

Propyl at carbon #5


Incorrect:

Ethyl at #4

Methyl at #7

Propyl at #5


Now we can name the structure. Here are some important rules to note:

-Numbers are separated from one another by commas, while numbers and words are separated by hyphens.

-Substituents are listed in alphabetical order such that the earliest in the alphabet is the first listed. IE: an ethyl group is written before methyl, ect. If there is a prefix (di, tri, ect) it is irrelevant to the order.

-The number(s) associated with each susbstituent are located directly infront of that substituent.

-If there is more than one of the same substituent, a prefix is placed before it's name to indicate how many are present
(di, tri, tetra, ect...). Additionally, a number will be listed for each if there are multiples. These can be on different carbon atoms, in such a case, the numbers are written in increasing order.


Thus, the name of our example compound is 6-ethyl-3,3-dimethyl-5-propylnonane


Practice:

What is the systematic name for the structure below?









Edited by afrekcan (11/25/14 10:46 PM)


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Invisible4HO-DMT
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Re: Organic Chemistry [Re: afrekcan]
    #20892838 - 11/26/14 11:33 AM (9 years, 2 months ago)

:bow2: thank you for your contributions. Many of us have been waiting for a update on this thread for a long time!


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Re: Organic Chemistry [Re: 4HO-DMT]
    #20894523 - 11/26/14 07:25 PM (9 years, 2 months ago)

I second that, thank you! I'm very happy this thread is alive.


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Re: Organic Chemistry [Re: kmetric]
    #20895864 - 11/27/14 06:08 AM (9 years, 2 months ago)

Is it 3,5 diethyl 2,6,8 trimethyl nonane?


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Re: Organic Chemistry [Re: wolf8312]
    #20896211 - 11/27/14 09:03 AM (9 years, 2 months ago)

Quote:

wolf8312 said:
Is it 3,5 diethyl 2,6,8 trimethyl nonane?




Indeed it is, however 3,5-diethyl-2,6,8-trimethylnonane is more proper.

Excellent choice of numbers! In a situation like this where there are two possibilities that yield the same set of numbers, the best name places the substituent that comes first in the alphabet at the lowest number.

I'm glad you all are interested. I should have more to post within the next few days.


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Re: Organic Chemistry [Re: afrekcan]
    #20898888 - 11/27/14 11:45 PM (9 years, 2 months ago)

You guys just lost me, how do you know which side to start from?


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Re: Organic Chemistry [Re: Razzldazzle]
    #20899401 - 11/28/14 04:50 AM (9 years, 2 months ago)

At first glance it seems that you have two identical parent chains but if you have two groups of equal importance (in this case 2 methyl on both possible parent chains both at position 2) appearing at the same point on both sides then you have to keep going and see which of the two possible chains has a substituent that appears sooner than on the other side.

If you and others really want to learn though best thing I would advise is to do what I myself am doing. Buy yourself a good O Chem book and then work through it chapter by chapter. If you come to something you don’t understand type it into YouTube and watch some videos. Then continue reading! In this day and age we have the best teachers money can buy teaching for free and right at our fingertips.

If you actually start getting into OC you will see why so many people dismiss organic chemistry as being a really difficult subject while others say in fact it is nowhere near as bad as it seems.

Some of the reaction mechanisms would be ridiculously difficult to understand if all you have is a book and a few classes with a professor a few times a week but really as with learning a language repetition is the key. With 'videos' you can stop, rewind, and replay them as many times as you like which is really vital for me -I think anyone really- as concentration needs to be utterly absolute and if you miss one sentence or even one word you can lose track of everything that the teacher is talking about.

Ive been learning for a few months and am just now getting to the exciting stuff- the reaction mechanisms. :tongue:

One question though...




In the Oxymercuration Demercuration reaction does anyone know why if mercury acetate :Hg(OAC)2 is an ionic bond and mercury only has two free valence electrons how is it then able to form an ionic bond with Oxygen(2) and yet still have a lone pair of electrons to then later use and form a bond with carbon?

I know that Oxygen is acting as a nucleophile and only sharing its own electrons but where then is mercury getting its positive charge from and why is it refered to as an ion if it has not lost any electrons?

Wouldnt the negative Oxygen ion's grab the electrons away from mercury and if not how then can mercury be a positively charged ion?

Hers a vid shes a great teacher first one explains the reaction I am talking about, the others are some links for noobs like me who just want to get started





(this one is not starting from the basic principles but the guy has videos on all different topics)


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Re: Organic Chemistry [Re: wolf8312]
    #20899791 - 11/28/14 09:42 AM (9 years, 2 months ago)

@wolf8312: Let me know if this helps or if you have further questions.

The bonds in mercury acetate are not ionic. However, before mercury will react with a double bond, it's bond to one of the acetate groups is broken and the acetate takes both electrons with it (essentially an ionic mechanism).
However, what i've just described is not terribly important to understanding the reaction. After the formation of HgAOc+, mercury still has a lone pair of electrons. These electrons then interact with a double bond (consists of two electrons).
This results in the formation of a three membered ring intermediate, called a mercurinium ion.


--------------------
 


Edited by afrekcan (11/28/14 03:31 PM)


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Re: Organic Chemistry [Re: afrekcan]
    #20900261 - 11/28/14 12:19 PM (9 years, 2 months ago)

Quote:

Let me know if this helps or if you have further questions.





Ah thanks dude I have plenty I'm sorry to say!

Quote:

The bonds in mercury acetate are not ionic.




Ah... 1.44! Shouldn’t have gone with the old metal + non-metal = ionic bond rule!

Quote:


However, before mercury will react with a double bond, it's bond to one of the acetate groups is broken and the acetate takes both electrons with it (essentially an ionic mechanism).




Yeah I should have been clearer I realized that one of the OAC groups withdraws from the bond, but as one mercury electron remains still bonded to the other OAC molecule from where do we then get the free lone pair (2 electrons) that goes onto attack the carbon? 

Mercury has only 2 available valance electrons, and even loses one of these to a leaving OAC (negatively charged because of this) group and then while still being bonded to another OAC group (with its only remaining electron) it somehow and from somewhere still has a free lone pair -2 electrons- to attack the carbon with and form the mercurinium ion? So what am I missing?

I could only understand this if Hg(OAC)2 in fact has and started with 4 valance electrons -1 each for both Hg-OAC bonds and a free lone pair for the attack. If it indeed only has two valence electrons however, loses one and still has 2 free to attack the carbon with then I am totally stumped!

Sorry if I’m being dense and totally missing something obvious here dude!
If it loses one electron to one OAC group and has one electron already involved in a Hg-0AC bond how can it have enough electrons left to attack the carbon with, as by my count it would have already lost one electron and have one still bonded to the Hg-OAC giving it no electrons left to attack with.

Quote:

One of these electrons initially "belongs" to mercury, so the net effect is that mercury loses an electron.





But is acetate (CH3COO-) not negative not because it gained a mercury electron but because it originally lost a hydrogen (when it was an acid CH3COOH and not a conjugate base CH3COO-) and was after this then bonded or reacted together with the mercury to form Hg(OAC)2?

Would this not explain why when the Hg and the one OAC group seperate that the Mercury is still left with one free lone pair and this is why we can then still have 2 valance electrons (not involved in the bond between itself and Oxygen) ready to then attack the carbon with?

I found some information online stating that Mercury acually very stubbornly refuses to share its valence electrons and also found this on answers.com

Quote:

Mercury was long believed not to use any other electrons in forming bonds and is called a post transition element.




Bit tired (3.15 in the morning here) so no time to delve too deep into post transition elements but Wiki mentioned something called mixed metallic bonding. Are we perhaps talking about a bond that operates in a manner of which I am not familliar? Is it perhaps a bond somehow apart from others which enables it to keep its own lone pair and yet still form covalent bonds somehow?

Or am I just missing something incredibly obvious?

This is driving me nuts lol!

I'm beat dude! Enough O chem for tonight been studying all day!

A drawing showing each and every electron involved in the bonds might really help me here dude!

Many thanks again!


--------------------
"I'm every nightmare you ever had. I am your worst dreams come true. I am everything you ever were afraid of."

Pennywise the dancing clown



Edited by wolf8312 (11/28/14 12:28 PM)


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Re: Organic Chemistry [Re: wolf8312]
    #20900295 - 11/28/14 12:28 PM (9 years, 2 months ago)

I have a "The Great Courses" video lecture class on Organic Chem from an actual O-Chem professor that I would love to give anyone who wants it, or maybe even upload it on here. Its 36 lectures and comes with a PDF guide book, here is the link to the website of the course. Its 16 GB so its a pretty big file. If anyone knows a way to either upload it here or send it to them let me know! 

Foundations of Organic Chemistry

Also, Here are some chemistry classes anyone can take for free online at any time from MIT

MIT Organic Chemistry 1

MIT Physical Chemistry 1

MIT Intro to Experimental Chemistry

Principles of Chemical Science

Here is an O-Chem Virtual Textbook

O-Chem Virtual Textbook



Edited by Razzldazzle (11/28/14 12:43 PM)


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Re: Organic Chemistry [Re: Razzldazzle]
    #20903839 - 11/29/14 09:55 AM (9 years, 2 months ago)

In a deoxymercuration reaction, the first step is nucleophilic attack of mercury acetate by the pi electrons in the carbon-carbon double bond.  This ejects an acetate group and is then followed by the lone pair of mercury attacking carbon to form the mercurinium ion.

Remember when doing mechainsms in organic chemistry, nothing ever just happens, you need to push electrons around.


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Re: Organic Chemistry [Re: Ice9]
    #20903871 - 11/29/14 10:05 AM (9 years, 2 months ago)

Yeah thanks dude but if you closely read what is written above you will see we are not so much talking about the reaction mechanism itself as whole or working out how it proceeds step by step but specifically talking about how mercury and the acetate ion interact together when accounting for the fact that mercury only contains 2 valence electrons.


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Re: Organic Chemistry [Re: wolf8312]
    #20904224 - 11/29/14 12:00 PM (9 years, 2 months ago)

To be honest I can't really answer your question wolf, however in my textbook mercury acetate is shown with 2 valence electrons in addition to the two bonds to acetate groups. I can post a picture later if you want, its more detailed than what I was able to find elsewhere.

However I think there may be a chance that what you found (mercury not wanting to share its 2 valence ect...) may be an explanation. I'm going to look into it over the next few days. If you find anything I'd be curious to know.


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Edited by afrekcan (11/29/14 12:05 PM)


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Re: Organic Chemistry [Re: afrekcan]
    #20904373 - 11/29/14 12:41 PM (9 years, 1 month ago)

Quote:


To be honest I can't really answer your question wolf, however in my textbook mercury acetate is shown with 2 valence electrons in addition to the two bonds to acetate groups. I can post a picture later if you want, its more detailed than what I was able to find elsewhere.




Don’t worry my good buddy I honestly cannot find anywhere online that can answer it either! Ha ha its driving me fucking nuts!

I cant work out if the lack of information online means that it is such a ridiculously easy and obvious answer that nobody has ever bothered to ask the question or if it is one so difficult that no-one has ever been able to solve it!

Mercury is a transition metal and so perhaps is a real wild card and I do get the feeling that the acetate bonds to it somehow without Hg sharing any electrons whatsoever!

Please if you ever do crack this though do get back to me! I have even sent an email to my dear mother asking for clarification (shes pretty good at chemistry ha ha)!

I see it as somehow that the mercury lone pair is not involved at all in bonding with the acetate ions and perhaps because mercury only has two valence electrons it is somehow naturally an unhappy and ready-made unstable electrophile! It will not share any electrons until it has gained a few here and there! I think in the reaction mechanism it is indeed referred to as electrophilic!

Even at the beginning of the reaction -when it is bonded to two acetate groups- in many depictions the mercury is represented with a lone pair of electrons!

I can only presume that although the bond is 'covalent' that in actual fact somehow the OAC is attracted only to an overall charge of the unstable mercury atom. :shrug:

At least for the sake of my own sanity that is how I am for the moment choosing to understand it!

Thanks for your help dude! Good vibes!


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Re: Organic Chemistry [Re: wolf8312]
    #20904528 - 11/29/14 01:32 PM (9 years, 1 month ago)

That explanation actually makes sense because the lone pair doesn't interact with anything until the formation of the carbocation (maybe it won't give them up except to a sufficiently positive charge..?).


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Re: Organic Chemistry [Re: afrekcan]
    #20904646 - 11/29/14 02:05 PM (9 years, 1 month ago)

Exactly! It seems to stubbornly do absolutely nothing with its lone pair until it is already 'electroned up' with 2 electrons from 2 other different bonds (carbon and Oxygen) and only then does it seem to decide to use its lone electron pair. I think somehow it needs to be bonded to other atoms before it will act.


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Re: Organic Chemistry [Re: wolf8312]
    #20906233 - 11/29/14 10:10 PM (9 years, 1 month ago)

The issue you are having here is that the electrons involved in the oxymercuration reaction are those from the 5d10 electron orbitals.  Specifically, in mercury(II) acetate the 5dz^2 orbital is empty, and the "lone pair" electrons are those of the 5dxz orbital.  The 6s2 electrons are not involved and as with many metals in the transition block filled s orbitals can be fairly inert.


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The reasonable man adapts himself to the world; the unreasonable one persists in trying to adapt the world to himself. Therefore, all progress depends on the unreasonable man. -- George Brenard Shaw


Edited by Ice9 (11/29/14 10:22 PM)


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Re: Organic Chemistry [Re: Ice9]
    #20906699 - 11/30/14 12:18 AM (9 years, 1 month ago)

Quote:

The issue you are having here is that the electrons involved in the oxymercuration reaction are those from the 5d10 electron orbitals.  Specifically, in mercury(II) acetate the 5dz^2 orbital is empty, and the "lone pair" electrons are those of the 5dxz orbital.  The 6s2 electrons are not involved and as with many metals in the transition block filled s orbitals can be fairly inert.






Ah thanks a lot dude a great help thank you!

Still a bit hazy and had to brush up on electron configurations for the inorganic elements! Really helped me actually cause it was something Id become rather rusty on!

I just spent 15 minutes drawing out the electron configeration diagram for mercury so we could all see what you are talking about only to find that the shroomerys disabled uploads (will post it later).

I can see clearly now that the 5f orbital is empty and that the 5d10 are the electrons that are involved in the bond.

Just to be clear the 'lone pair' are the inert 6 shell electrons, but the bond between the mercury and the acetate is coming from the electrons in the 5d10 5th shell right?

So the acetate forms a covalent bond with the orbitals in the 5th shell while leaving the lone pair in the sixth shell free? 

None of these electrons are removed by the acetate when it withdraws right?

Most important thing now is that I know is we are dealing with an anomaly, so I can stop worrying!


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Re: Organic Chemistry [Re: wolf8312]
    #20907586 - 11/30/14 09:43 AM (9 years, 1 month ago)

Mercury acetate is an ionic compound, with mercury having a formal 2+ charge, when the acetate group leaves, it takes both its electrons with it (otherwise we would be making radical species).  In this reaction the lone pair are actually the electrons in the 5dxz orbital, technically electrons in the 6s orbital are actually lower energy than electrons in the 5d orbitals (6s orbital fills with electrons before the 5d orbital).  Also, because mercury is in the 2+ oxidation state the 5d orbital is 5d8--->5d10 from the electrons from the 2 acetate groups.


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Re: Organic Chemistry [Re: Ice9]
    #20907886 - 11/30/14 11:18 AM (9 years, 1 month ago)

Quote:

Mercury acetate is an ionic compound, with mercury having a formal 2+ charge, when the acetate group leaves, it takes both its electrons with it (otherwise we would be making radical species).




Sorry when you say 'its' you mean acetate takes its own eletrons back or withdraws with two electrons from mercurys 5 shell? 

Quote:

Also, because mercury is in the 2+ oxidation state the 5d orbital is 5d8--->5d10 from the electrons from the 2 acetate groups.





Sorry I dont really understand what you mean by this.

Are you sure its ionic?

I have read conflicting information about this and now don’t know what to believe!

Also the mercury acetate in the oxymercuration demercuration video I provided above only represents the acetate ion after having been detached during the first step with seven electrons and surely one of these must have come from the hydrogen bond what with the acetate originally being the conjugate base of vinegar CH3COOH no?

Ive found a guy online who also said this:

Quote:


From my experience, Mercury (II) Acetate is one of these – unfortunately many, many – examples which you find in many forms in different database – and it is very hard to normalize or correct them to a unique representation – probably because it isn’t clear whether the type of Hg-O bond is ionic or covalent, or the rules are complex, or change from metal to metal or ligand/ion to ligand/ion.




Mercury also has an electronegativity of 2, Oxygen, 3.44 with a difference of 1.44 which I thought was supposed to mean it is closer to covalent than ionic? :shrug:

Any chance you could provide a diagram or link to show what you mean so as to illustrate the movement of the acetate and oxygen electrons?


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Re: Organic Chemistry [Re: wolf8312]
    #20913937 - 12/01/14 07:07 PM (9 years, 1 month ago)

Organometallics is its own little subset of organic chemistry too. I could ask my advisor about it if you would like, but my school doesn't really have any research going on in that field right now. It's the generic cancer/climate/biochem research here.


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Re: Organic Chemistry [Re: Thebooedocksaint]
    #20914774 - 12/01/14 09:42 PM (9 years, 1 month ago)

Yeah thanks dude surprised by how little information there is about this. I asked the teacher from the videos I provided  about it but she said it was not undergraduate level and so something she doesent teach. I asked her if the bonds were ionic or covalent but she didn't reply. Guess that means :shrug:


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Re: Organic Chemistry [Re: wolf8312] * 1
    #20916262 - 12/02/14 09:53 AM (9 years, 1 month ago)

Mercury acetate is not an organometallic compound, those contain metal-carbon bonds and usually involve transition metals.  And yes, it is very complex chemistry due to number/geometry of coordination sites among others factors.  As to whether the bonds in mercury acetate are ionic, they are, they may have some covalent character (it is a continuum, not a discrete measure).  It is also somewhat irrelevant to the oxymercuration reaction. 

Should note that there are many cleaner, more environmentally friendly methods of hydrating a carbon carbon double bond, even ones where you can not only control regiochemistry, but also the stereochemistry of the product.


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Re: Organic Chemistry [Re: Ice9]
    #20918042 - 12/02/14 04:03 PM (9 years, 1 month ago)

Noted, I suppose I didn't look back at the molecule in question when I made that comment. "Metalorganic" instead.


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Re: Organic Chemistry [Re: Thebooedocksaint]
    #20994159 - 12/18/14 01:27 PM (9 years, 1 month ago)

Hello chemistry students,


I want to extend an invitation to each of you. Join the "Guess The Fungi/Mushroom Chemical!" thread.


You can teach, but you have to be an excellent teacher!


http://www.shroomery.org/forums/showflat.php/Number/19336895/fpart/1/vc/1


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Re: Organic Chemistry [Re: The Lightning]
    #20994986 - 12/18/14 04:17 PM (9 years, 1 month ago)

Over this break I'll start discussion on functional groups, and connect them back to previously understood classes or organic compounds. Will build off the fact this thread has already covered saturated carbon-hydrogen molecules, cover unsaturated Carbon Hydrogen molecules and then begin to learn about organic molecules containing more than just carbon and Hydrogen. We will cover whatever material I can cover over winter break, and then if my next semester is as relaxed as I expect it to be I may continue with roughly monthly contributions of lecture, and at least weekly responses to questions. As I've said before I'm no organic chemist so if you think I'm wrong call me on it, but I can at the vary least continue this roughly descriptive style of course.

I will use chem doodle for drawing structures.

Expect an update this weekend/early next week,


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Re: Organic Chemistry [Re: Thebooedocksaint]
    #21015938 - 12/23/14 08:52 AM (9 years, 1 month ago)

Whoa, can't wait for the next update! :crazy:
Is there any recommended OC books which won't make me fall asleep too soon? (Since I only have Brady at home). Thanks beforehand! :blush:


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Re: Organic Chemistry [Re: lavallium] * 1
    #21019295 - 12/23/14 10:02 PM (9 years, 1 month ago)

Yes without any doubt what so ever get organic chemistry as a second language lots of practice problems to work on which is really important if you don't have a teacher setting you homework! Best book I've found so far!


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Re: Organic Chemistry [Re: wolf8312]
    #21095420 - 01/10/15 03:21 AM (9 years, 20 days ago)

Just want to add to this! Organic chemistry as a second language is fricking brilliant!

All the other books I have are useful but it was only when going back through and working on problems such as resonance and chair structures (etc) that I came to realize how piss poor my grasp on everything I had learned actually was. Sometimes I wont even understand an explanation very well but if I spend a while working through the problems myself before long I will understand.

With all the other books you will still need to buy others (work books) and take in information from other sources on or offline.

With organic chemistry as a second language however you are provided with all the information you will ever need to actually learn organic chemistry yourself!

Honest to God its better than anything I have found! If you really want to learn O chem just get it!

You should also buy yourself an atomic model set as well though to help you get a feel for the stereochemistry! 

The most important thing is to get a firm grasp on the basics before deciding to move onto the reaction mechanisms themselves. I am so glad I found it and dont even use youtube anymore!


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InvisiblePanzerCubed
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Re: Organic Chemistry [Re: wolf8312]
    #21245924 - 02/08/15 10:07 PM (8 years, 11 months ago)

Thanks for doing this, ill be watching this thread.


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OfflineSeaShrooms
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Re: Organic Chemistry [Re: PanzerCubed]
    #21249299 - 02/09/15 04:15 PM (8 years, 11 months ago)

:cheers: Watching


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OfflineNightontheSun
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Re: Organic Chemistry [Re: Earthspirit]
    #21351493 - 03/02/15 10:59 AM (8 years, 10 months ago)

I love it, I'm looking forward to your future lessons. So far your very straight forward and explain everything highly simplisticly making everything easy to understand.

I have some self taught organic chem. as do a lot of people on this site and I have wanted to take chemistry at the local community college so this would be a great start. Anything to keep me from going into class blind would be highly sought after. Keep up the great work!


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Offlinerxb
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Re: Organic Chemistry [Re: NightontheSun]
    #21411511 - 03/15/15 01:31 PM (8 years, 10 months ago)

this should be a seperate subforum where people can post relivant info as lessons.


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. i cleaned a mold contaminated live culture and saved it. (might have useful applications)

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OfflineSeaShrooms
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Re: Organic Chemistry [Re: rxb]
    #21411575 - 03/15/15 01:51 PM (8 years, 10 months ago)

Agreed, as important as it is to this forum...


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